TB-Profiler result

Run: ERR2229791
Summary

Run ID: ERR2229791

Sample name:

Date: 31-03-2023 17:35:37

Number of reads: 16564

Percentage reads mapped: 22.14

Strain: lineage4.9

Drug-resistance: RR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761127 p.Ser441Ala missense_variant 0.67 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.55 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.83 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 8264 c.963T>C synonymous_variant 1.0
gyrA 8267 c.966G>C synonymous_variant 1.0
gyrA 8294 c.993T>C synonymous_variant 0.4
gyrA 8316 p.Thr339Glu missense_variant 0.4
gyrA 8320 p.Ser340Asn missense_variant 0.4
gyrA 8324 c.1023T>C synonymous_variant 0.4
gyrA 8325 p.Gly342Ser missense_variant 0.4
gyrA 8330 c.1029C>G synonymous_variant 0.4
gyrA 8339 c.1038A>G synonymous_variant 0.4
gyrA 8354 c.1053G>C synonymous_variant 0.4
rpoB 761036 c.1230G>C synonymous_variant 1.0
rpoB 761037 c.1231T>C synonymous_variant 1.0
rpoB 761051 c.1245G>C synonymous_variant 0.8
rpoB 761054 c.1248G>C synonymous_variant 0.8
rpoB 761060 c.1254C>G synonymous_variant 0.8
rpoB 761064 p.Ala420Ser missense_variant 0.8
rpoB 761084 c.1278C>G synonymous_variant 0.4
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.4
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.4
rpoB 761102 c.1296A>G synonymous_variant 0.4
rpoB 761132 c.1326G>C synonymous_variant 0.67
rpoB 761133 c.1327T>C synonymous_variant 0.67
rpoB 761974 p.His723Leu missense_variant 0.8
rpoB 762003 p.Asn733Gln missense_variant 0.8
rpoB 762008 c.2202C>G synonymous_variant 0.8
rpoB 762009 p.Leu735Met missense_variant 0.8
rpoB 762015 p.Glu737Ser missense_variant 0.8
rpoB 762020 p.Glu738Asp missense_variant 0.8
rpoB 762029 c.2223C>G synonymous_variant 0.8
rpoB 762053 c.2247T>C synonymous_variant 0.8
rpoB 762062 c.2256T>C synonymous_variant 0.8
rpoB 762065 c.2259T>C synonymous_variant 0.8
rpoB 762849 p.Tyr1015Asp missense_variant 1.0
rpoB 762855 p.Val1017Ile missense_variant 1.0
rpoB 762858 p.Thr1018Ser missense_variant 1.0
rpoC 762863 c.-507T>G upstream_gene_variant 1.0
rpoB 762870 p.Met1022Gln missense_variant 1.0
rpoB 762879 p.Met1025Leu missense_variant 1.0
rpoC 762929 c.-441G>C upstream_gene_variant 0.89
rpoC 762980 c.-390T>C upstream_gene_variant 0.88
rpoC 762983 c.-387C>T upstream_gene_variant 0.88
rpoC 762989 c.-381G>C upstream_gene_variant 0.88
rpoC 762995 c.-375G>C upstream_gene_variant 0.83
rpoB 763005 p.Cys1067Val missense_variant 0.75
rpoB 763014 p.Met1070Leu missense_variant 0.75
rpoB 763017 p.Gln1071Glu missense_variant 0.75
rpoC 763022 c.-348C>G upstream_gene_variant 0.75
rpoC 763028 c.-342T>C upstream_gene_variant 0.75
rpoC 763031 c.-339T>G upstream_gene_variant 0.75
rpoB 763050 p.Leu1082Met missense_variant 1.0
rpoC 763501 p.Asp44Glu missense_variant 1.0
rpoC 763504 c.135C>T synonymous_variant 1.0
rpoC 763511 p.Cys48Asp missense_variant 1.0
rpoC 763517 p.Lys50Arg missense_variant 1.0
rpoC 763534 c.165T>C synonymous_variant 1.0
rpoC 763546 c.177A>G synonymous_variant 1.0
rpoC 763570 c.201G>C synonymous_variant 0.83
rpoC 763621 c.252C>G synonymous_variant 0.88
rpoC 763633 c.264T>C synonymous_variant 0.83
rpoC 763660 c.291T>G synonymous_variant 0.86
rpoC 763675 c.306C>G synonymous_variant 0.83
rpoC 763696 c.327T>C synonymous_variant 0.8
rpoC 764449 c.1080G>C synonymous_variant 1.0
rpoC 764497 c.1128A>G synonymous_variant 0.75
rpoC 764498 p.Ser377Ala missense_variant 0.75
rpoC 764507 p.Ala380Ser missense_variant 0.75
rpoC 764521 c.1152T>C synonymous_variant 0.83
rpoC 764527 c.1158C>G synonymous_variant 0.83
rpoC 764533 c.1164C>T synonymous_variant 0.71
rpoC 764536 c.1167G>C synonymous_variant 0.75
rpoC 764539 c.1170C>G synonymous_variant 0.78
rpoC 764560 c.1191T>C synonymous_variant 0.67
rpoC 764566 c.1197C>G synonymous_variant 0.67
rpoC 764572 c.1203G>C synonymous_variant 0.67
rpoC 764575 c.1206T>G synonymous_variant 0.67
rpoC 764578 c.1209C>G synonymous_variant 0.67
rpoC 764581 c.1212T>C synonymous_variant 0.57
rpoC 764582 p.Leu405Met missense_variant 0.57
rpoC 764611 c.1242G>C synonymous_variant 0.71
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.71
rpoC 764632 c.1263T>C synonymous_variant 0.71
rpoC 764635 c.1266C>G synonymous_variant 0.71
rpoC 764650 c.1281G>C synonymous_variant 1.0
rpoC 764665 c.1296C>G synonymous_variant 1.0
rpoC 764677 c.1308C>G synonymous_variant 1.0
rpoC 764681 p.Leu438Met missense_variant 1.0
rpoC 764706 p.Leu446Gln missense_variant 1.0
rpoC 764713 c.1344G>C synonymous_variant 1.0
rpoC 764731 c.1362G>C synonymous_variant 1.0
rpoC 764746 c.1377G>C synonymous_variant 1.0
rpoC 764758 c.1389C>G synonymous_variant 1.0
rpoC 764764 c.1395T>C synonymous_variant 1.0
rpoC 764780 c.1411_1412delAGinsTC synonymous_variant 1.0
rpoC 764791 c.1422C>G synonymous_variant 1.0
rpoC 764804 p.Gln479Phe missense_variant 1.0
rpoC 764812 c.1443C>G synonymous_variant 1.0
rpoC 764815 c.1446A>G synonymous_variant 1.0
rpoC 764818 c.1449G>C synonymous_variant 1.0
rpoC 764824 c.1455T>C synonymous_variant 1.0
rpoC 764830 c.1461C>G synonymous_variant 1.0
rpoC 764833 c.1464A>G synonymous_variant 1.0
rpoC 764837 p.Val490Ile missense_variant 1.0
rpoC 764843 p.Ala492Thr missense_variant 1.0
rpoC 764858 c.1489T>C synonymous_variant 1.0
rpoC 764863 c.1494G>C synonymous_variant 1.0
rpoC 764872 c.1503A>C synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781766 c.207C>T synonymous_variant 0.67
rpsL 781793 c.234G>C synonymous_variant 0.67
rpsL 781796 p.Met79Ile missense_variant 0.67
rpsL 781802 c.243G>C synonymous_variant 0.4
rpsL 781814 c.255C>T synonymous_variant 0.4
rpsL 781817 c.258G>T synonymous_variant 0.4
rpsL 781829 c.270G>C synonymous_variant 0.5
rpsL 781832 c.273T>C synonymous_variant 0.5
rpsL 781835 c.276T>C synonymous_variant 0.5
rpsL 781841 c.282C>G synonymous_variant 0.5
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.75
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.75
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.83
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.86
rrs 1472224 n.379G>A non_coding_transcript_exon_variant 0.22
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.75
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.67
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.67
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.67
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.67
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.67
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.67
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.62
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.5
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.45
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.44
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.44
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.44
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.44
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.44
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.4
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.67
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.67
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.67
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.67
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.8
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.86
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.83
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.83
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.83
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.83
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.56
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.45
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.45
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.45
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.38
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.62
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.62
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.6
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.67
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.6
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.5
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.5
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.5
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.5
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.43
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.43
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.43
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.43
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.82
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.82
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.73
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.73
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.89
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.89
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.9
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.9
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.86
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 1.0
rrl 1474284 n.631_633delCCT non_coding_transcript_exon_variant 1.0
rrl 1474293 n.637_651delCCTCTCCGGAGGAGG non_coding_transcript_exon_variant 1.0
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 1.0
rrl 1474348 n.691C>T non_coding_transcript_exon_variant 1.0
rrl 1474351 n.694G>T non_coding_transcript_exon_variant 1.0
rrl 1474353 n.696A>T non_coding_transcript_exon_variant 1.0
rrl 1474354 n.697C>T non_coding_transcript_exon_variant 1.0
rrl 1474355 n.698A>C non_coding_transcript_exon_variant 1.0
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 1.0
rrl 1474384 n.727C>T non_coding_transcript_exon_variant 1.0
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 1.0
rrl 1474406 n.749T>G non_coding_transcript_exon_variant 1.0
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 1.0
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 1.0
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 1.0
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.67
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.67
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.67
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.5
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.5
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.5
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.67
rrl 1474633 n.977_981delTCACC non_coding_transcript_exon_variant 0.67
rrl 1474640 n.983_984insTTGCT non_coding_transcript_exon_variant 0.67
rrl 1474658 n.1001A>T non_coding_transcript_exon_variant 0.67
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.67
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.67
rrl 1474675 n.1018C>T non_coding_transcript_exon_variant 0.67
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.67
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.67
rrl 1474691 n.1034A>T non_coding_transcript_exon_variant 1.0
rrl 1474709 n.1053_1056delTGGT non_coding_transcript_exon_variant 1.0
rrl 1474717 n.1060_1061insGTTTT non_coding_transcript_exon_variant 1.0
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 1.0
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 1.0
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 1.0
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 1.0
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 1.0
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 1.0
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 1.0
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 1.0
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 1.0
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 1.0
rrl 1474836 n.1179A>C non_coding_transcript_exon_variant 0.4
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 1.0
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 1.0
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 1.0
rrl 1475515 n.1858G>A non_coding_transcript_exon_variant 0.67
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 1.0
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 1.0
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 1.0
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 1.0
rrl 1475752 n.2095C>T non_coding_transcript_exon_variant 1.0
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 1.0
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 1.0
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 1.0
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 1.0
rrl 1475769 n.2112_2113insC non_coding_transcript_exon_variant 1.0
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 1.0
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 1.0
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 1.0
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 1.0
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 1.0
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 1.0
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 1.0
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 1.0
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 1.0
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 1.0
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 1.0
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 1.0
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 1.0
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 1.0
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 1.0
rrl 1475998 n.2341C>T non_coding_transcript_exon_variant 1.0
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 1.0
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 1.0
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.92
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.92
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.86
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.8
rrl 1476519 n.2862C>T non_coding_transcript_exon_variant 0.75
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.67
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.67
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.67
rrl 1476530 n.2873C>A non_coding_transcript_exon_variant 0.67
rrl 1476534 n.2877A>T non_coding_transcript_exon_variant 0.67
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.67
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.67
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.67
rpsA 1833955 c.414G>C synonymous_variant 1.0
rpsA 1833961 c.420C>G synonymous_variant 1.0
rpsA 1834285 c.744G>C synonymous_variant 1.0
rpsA 1834294 c.753G>C synonymous_variant 1.0
rpsA 1834298 p.Gln253Glu missense_variant 1.0
rpsA 1834303 c.762T>C synonymous_variant 1.0
rpsA 1834306 c.765T>C synonymous_variant 1.0
rpsA 1834307 p.Asp256Gln missense_variant 1.0
rpsA 1834333 p.Asp264Glu missense_variant 1.0
rpsA 1834336 c.795C>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 1.0
PPE35 2170053 p.Thr187Ser missense_variant 1.0
clpC1 4038563 c.2142C>T synonymous_variant 1.0
clpC1 4038566 p.Ile713Val missense_variant 1.0
clpC1 4038596 p.Lys703Glu missense_variant 1.0
clpC1 4038602 c.2103G>C synonymous_variant 1.0
clpC1 4039886 c.819C>G synonymous_variant 1.0
clpC1 4039898 c.807C>G synonymous_variant 1.0
clpC1 4039904 c.801A>G synonymous_variant 1.0
clpC1 4039916 c.789T>G synonymous_variant 1.0
clpC1 4040057 c.648C>T synonymous_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0